What Programs Will Stop?

One of the biggest impacts will be the inability for the National Institutes of Health (NIH) to move into Phase II clinical trials. The organization began Phase I today, but it needs to start ramping up to prepare for Phase II trials to start as early as January 2017.

"When I say we're going to run out of money soon I mean really soon," National Institute of Allergy and Infectious Diseases (NIAID) Director Dr. Anthony Fauci said on a press call today.

In addition, Burwell outlines in her letter that BARDA (Biomedical Advanced Research and Development Authority) will exhaust the $85 million it received in short-term funding by the end of August. BARDA is responsible for funding private-sector partners in development of medicine and vaccines.

The Centers for Disease Control will also use all of its domestic funding by the end of September, which will mean no more money dedicated to fighting local Zika outbreaks and emergency response teams.

Where Is That Money Coming From?

Back in April, the administration diverted $589 million from funds intended to combat Ebola to help fight Zika. Of that, $78 million was set aside for international response and $138 million went to the State Department and United States Agency for International Development (USAID).

From the money HHS was able to use domestically, $374 million was split between the CDC, NIH and BARDA. Of the $222 million the CDC received as the nation's first line of defense, $123 million has already been awarded or obligated. The government agency expects the rest to run out by the end of September.

Why Couldn't Congress Come to an Agreement?

The Senate did come to a bipartisan agreement in May for around $1.1 billion. The House approved its own $1.1 billion deal in June, but without support from Democrats and to much controversy.

Democrats argued they were left out of the negotiations and say the funding steals money from other health programs. The president even threatened to veto the deal, with Deputy Press Secretary Eric Schultz telling reporters at the time the bill "would steal money from other critically important public health priorities."

"We urge Republicans to stop turning this into a political football and to actually get to work to come up with proposals that will serve the American people," he said.

The House version remains stalled in the Senate by a Democratic-led filibusterer.

So Why Won't Congress Come Back and Solve the Problem?

Senate Majority Leader Mitch McConnell's (R-KY) office told ABC News in response to the letter: "The House passed the funding bill already but it continues to be blocked in the Senate by a Democrat-led filibuster. We would love for them to end that filibuster and pass the bill, but it doesn’t sound like they’re prepared to do that."

His office added: "[The letter] says they have funds that will last through the end of the fiscal year that are not yet allocated."

A spokesman for McConnell's office also acknowledged that "it’s true that it [the bill] wasn’t passed with bipartisan support -- because they filibustered the bill. We can’t pass it if Dems block it. And clearly they believed that guaranteeing funding for Planned Parenthood was more important than providing funds for Zika now. That was a choice they made."

"We hope Senate Democrats read the Obama administration’s letter and have a change of heart on their dangerous filibuster of the House-passed $1.1 billion package to fight Zika," AshLee Strong, press secretary for Speaker Ryan, said.

Minority Leader Sen. Harry Reid (D-NV) said in a statement following the announcement of Zika in Miami Friday that “things will only get worse if Republicans continue their refusal to work with Democrats on a bipartisan response.”

“Instead of dealing with this months ago as Democrats demanded, Republican leaders did nothing and made the shameful decision that a seven-week vacation was more important than bipartisan action to stop the Zika virus,” he said in a statement. “The House and Senate must return to Washington immediately to provide the funding public health officials need to protect the American people. This news should be a wakeup call to Republicans to start taking this threat seriously.”